Please use more meaningful thread titles - like "placing tiles removes existing background" - so people can have an idea of what you need help with even before opening the thread (I know if I can't help with something, I don't bother looking at it, which means I can get more done in the same amount of time).
To elaborate on the above, the A tiles are ground tiles. Apart from a few of them on the A2 tab, anything you draw from the A tab will replace other A tiles. B-E tiles are the upper layer, and will be drawn over the ground tiles. In general, you wouldn't put tiles with transparent areas on the A tab.